Shaded From The Truth
by Joshweiser22
Summary: Another one of my fanfictions in which Derpy Hooves helps out Princess Celestia's mission that involves Dr. Whooves and Colgate. But what Derpy Hooves doesn't know is if this is really all part of there plan. Or is there someone else involved?
1. The Recruit

**Chapter 1: The Recruit**

"Hi there! I'm Derpy Hooves! Um, while I was giving the mail to the ponies, I noticed a piece of paper with my name on it and it said to come here." The derp-eyed pony said in front of a door. The door opened and a face immerged from a shadow. It said "Come in. Quick." Derpy looked confused, more than usual, but decided to go inside anyway.

Once inside, everything was very dark. Derpy looked around but didn't see anything except for the hooves of the pony right in front of her. The pony stopped and Derpy heard teeth being brushed. "Colgate, Derpy Hooves has arrived." Said the stranger pony. The brushing suddenly stopped and a door opened. Derpy saw another pony come out of nowhere. Probably a door but it was too dark to see. "She is going to be quite an ally to us in our mission." The first pony said. "Quite. She's going to be perfect." The pony, who Derpy figured to be Colgate based on the first pony's comment, said.

Derpy heard a flick and suddenly all the lights turned on. The two ponies were in a full view. A brown pony with an hourglass cutie mark stood right in front of Derpy and a blue and white pony, also with an hourglass cutie mark stood next to the brown pony. "I am Dr. Whooves." The brown pony said "And this is Colgate" he continued, pointing to the blue and white pony. Derpy had a dazed look on her face, still confused about everything that was going on. And then, in an instant she began smiling and said "Pleased to meet you!" as if she had forgotten all the eerie greetings that Dr. Whooves and Colgate had just put her through.

Dr. Whooves continued "We are on a top secret mission issued by the Princess. You are a key player to this mission and can help us, however, the Princess doesn't know it. We must bring you to her to get her permission." "I get to meet Princess Celestia! Cool! Do you think she'll have muffins?" Derpy asked. "I'm not too sure. But here, take this." Colgate said, tossing her a muffin. Derpy went wide eyed and mouthwatering. Dr. Whooves gave out a sigh of relief when he saw how Colgate solely focused on the muffin part of Derpy's comment and not the Princess Celestia part. She would be meeting Princess Celestia now but she still had no idea what was _actually _going on.


	2. The TARDIS

**Chapter 2: The TARDIS**

They climbed aboard the train to Canterlot and went straight for the castle without any side tracts. At the front of the castle, the guards let them in without any hesitation and they made their way to Princess Celestia.

"Does she know?" asked Princess Celestia pointing to Derpy as they walked in her room. "Not yet, your highness. But Colgate and I believe she'll be very valuable to the mission and we ask for your permission to include her." informed Dr. Whooves. "Very well. I'll choose to trust my people and I'll have faith in you. She may be debriefed." Princess Celestia responded.

Dr. Whooves looked to Derpy "Our mission, and now yours so you chose to accept it, is to make sure the changeling threat is gone. I'll be able to explain more when we return to Ponyville as we have collected much more information." The three headed back to Ponyville and back inside Dr. Whooves' house.

"We have been at this for quite some time now and still no luck." Dr. Whooves continued now at his house. Even the Princess did not know how we could trace her. Instead, we decided to get information from another source. We traveled to the Princess' castle in the middle of the night and found her sister inside. We asked her how we might be able to find the changelings and she said that the best way is to go to the source of the problem. Of course, the source of the problem already happened and is gone now. This is why she gave us an incredible idea. Time travel."

"Princess Luna told you that? But isn't it dangerous?" Derpy asked. "Maybe. Maybe not. But she offered it so who are _we_ to decline?" Colgate responded. "However, for time travel to be possible, one must need a time machine, no?" Dr. Whooves said, heading over to a rectangular object with a sheet on top. "Ooo! What's that?" asked Derpy. "This my fair mare, this is the Time And Relative Dimension In Space – more commonly known as…" began Dr. Whooves "the TARDIS" he continued as he pulled the sheet off the rectangular object revealing a police box.

"But, that says Police Box on it." Derpy stated. "Yes, but it's the TARDIS." Dr. Whooves argued. "So it's a TARDIS Police Box?" Derpy asked. "No, it's just a TARDIS." Dr. Whooves argued back. "What's a Justuh TARDIS?" Derpy asked, still very confused on what was going on. Dr. Whooves let out a big sigh. "Derpy Hooves. This is a TARDIS. Say it with me. TAR-DIS." "TAR-DIS." Derpy mimicked. "Good. Now let's go inside the TARDIS." Dr. Whooves ordered. "Wait, one question." Derpy stated and then asked "What's a TARDIS?" Colgate facehoofed. Dr. Whooves was now beyond annoyed. "It's a time machine! Now get in the TARDIS!" he yelled. Dr. Whooves was normally a happy fellow, unless he was around pears, or in this case, Derpy.

Derpy's eyes started getting watery "P-please don't yell at me sir. I don't like getting yelled at." Derpy said trying not to cry even though a few tears came out. Colgate started hugging Derpy "There, there." Colgate looked to Dr. Whooves "If you want this to work, you're going to have to be patient!" Dr. Whooves was rubbing his forehead. "Alright. Come on." He said, walking into the TARDIS. Colgate and Derpy soon followed.

Once inside, it was incredibly bigger than it was on the outside. "We are going back to the date of the wedding which is the same day the changelings arrived." Dr. Whooves said. "And once there, we'll finally be able to rid ourselves of them." Colgate said letting out a snicker that sounded much different than a normal laugh. Derpy, of course, couldn't notice the different, though, but if she had, she might've been able to find out who Colgate really meant to get rid of.


	3. The Source

**Chapter 3: The Source**

Dr. Whooves sent the TARDIS straight for the past in Canterlot. This was the location of Shining Armor and Cadence's wedding. The leader of the changelings, Queen Chrysalis, however, had other plans for them and had trapped Cadence underground. Chrysalis then took Cadence's form and was using Shining Armor's love for Cadence to overpower Princess Celestia. The TARDIS arrived right outside the castle and they could hear Cadence singing something about this day being perfect. They did, however, know that at this point, the real Cadence was still underground so this had to be Queen Chrysalis.

"Alright, everypony out. We have work to do. We can't let anypony see us and if somepony does, we must act as if we are from this time and know nothing of future events that are to transpire with the wedding. Understand?" ordered Dr. Whooves. Colgate nodded. "What does transpire mean?" Derpy asked. "Just don't say anything." Dr. Whooves replied. The trio got out of the TARDIS and headed to a window in the castle. They could see the Chrysalis Cadence laughing maniacally. She turned around and the three immediately ducked down so she wouldn't see them. They went around and entered the castle through the main entrance.

Dr. Whooves told the guards that they were there for the wedding and they let them in. Once inside, all that was left was for battle to begin. "We came here a little too early so we must wait." Dr. Whooves told them. Everypony gathered in the wedding room. Chrysalis Cadence and Shining Armor were about to get married when the real Cadence suddenly burst in with a purple pony who Dr. Whooves knew to be none other than Twilight Sparkle. "That's Twilight Sparkle. She's a very important part of this plan, I'll tell you more later." Dr. Whooves whispered to Derpy.

Soon, the Chrysalis Cadence was changing into her true form. Black with holes in her. She began to have a fight with _the_ Princess Celestia and Chrysalis won. Derpy cringed at seeing this for a second time but nopony seemed to notice. That's when havoc begun. An army of changelings flew in and started attacking the ponies although there were six who seemed to be fighting back. Dr. Whooves looked to Derpy. "Those are the ponies that represent the six elements of harmony: Loyalty, Honesty, Kindness, Laughter, Generosity, and Magic. They sure had a big help on removing the changeling threat." He said. "Yeah, and we have to make sure they don't like, go back in time or something crazy like that would ever happen." Colgate said followed by Dr. Whooves giving her a stern look.

Once most of the changelings were gone, Cadence and Shining Armor were re-united. They put their horns together and began using their own magic to defeat Queen Chrysalis. She got blown away with the rest of her changeling army. It was now Dr. Whooves' time. The three went back out and went straight into the TARDIS. They used it to follow where the changelings were being sent. Eventually, they stopped getting thrown back and all fell. They seemed to be in a changeling colony. Dr. Whooves somehow knew exactly where everything was here. So did Colgate. Derpy just followed them, in fear. Dr. Whooves went straight for Queen Chrysalis and she moaned at the sight of another pony.

"I've had enough of you ponies. What more do you want? You already defeated me." Queen Chrysalis said. "Yes, and we're here to make sure you don't come back. But we're on friendly terms. Please come with me." Dr. Whooves said. Dr. Whooves led Queen Chrysalis to a closed up hut and told both Colgate and Derpy to wait outside. Queen Chrysalis and Dr. Whooves sat down face to face.

Dr. Whooves began talking "Make sure you don't come back? Phooey. I need you and you need me and just so that you know I'm telling the truth…" his body began changing. He changed from brown to black. He grew very long horn. Holes started appearing in his hooves. Queen Chrysalis looked at him, or what was actually more appropriate, her. She thought maybe there was some sort of mirror. Changelings couldn't change into other changelings so she knew it wasn't some changeling from her army. It was no mistake. Queen Chrysalis was looking at none other than herself.


	4. The Throne

**Chapter 4: The Throne**

Queen Chrysalis continued to look straight at the newly transformed Dr. Whooves, deep with curiosity. "Surprised?" Dr. Whooves, in the form of Queen Chrysalis, said "Don't you think you're capable of such a thing as time travel?" it continued. Queen Chrysalis looked at him/her "Are you saying you're me from the future?" The other Queen Chrysalis nodded. She was indeed Queen Chrysalis from the future and had just taken Dr. Whooves' form!

The future Queen Chrysalis continued "And as I said before, we need each other right now. The two of us can go back in time again! Then there will be four of us total! The original, me from a few minutes ago while I was waiting for you to be defeated, you, and I! Four master changelings against a few ponies! We'll be unstoppable!" The past Queen Chrysalis' grin grew until she joined in on an evil laughter than the future one had started. The future Queen Chrysalis began telling the past Queen Chrysalis about who the two ponies she had brought were.

Colgate was actually one of the changelings in her army and Derpy Hooves…was probably the most important of them all. If they hadn't distracted Princess Celestia with Derpy, she would have realized that they were traveling into the past and would try to stop them. To avoid that, they added Derpy to the team, giving more work for the Princess to cover and hide from her subjects. They had to tell Derpy that Princess Luna had suggested time travel just so she would go along with it even though it wasn't true at all. Finally, if they had brought any other pony, they would have realized what the changelings were up to and would have stopped them dead in their tracks. Only Derpy could be that oblivious. Now that there were two Queen Chrysalises, they could go back to the TARDIS, without any hesitation of being caught by Derpy because she was really no match for two master changelings and an entire army. The two stepped out of the hut.

"Huh?" Derpy said as she saw two Queen Chrysalises step out. "Oh don't you get it Derpy Hooves? You've been playing for us the entire time." The future Queen Chrysalis said. Colgate put her hooves on Derpy's neck. "Take her away, minion!" said the past Queen Chrysalis. Colgate nodded, transformed into an army changeling and flew her away, deeper into the changeling colony.

"Well. Now that that's done, we can proceed to the TARDIS!" said future Chrysalis. "May ask what IS this TARDIS?" asked the past Chrysalis. The future Chrysalis explained that the TARDIS was Dr. Whooves' time machine and that she transformed into him so that she could use it. They got inside and headed back for the past once more. This time, they were a little farther behind the TARDIS that came here before.

They went up to the Queen Chrysalis stepping out of the TARDIS who at this time was still in her Dr. Whooves form and with Derpy Hooves and the changeling in Colgate's form. "Send her back to the colony." Queen Chrysalis told the changeling in Colgate's form. Like before, or after it should be said, Colgate transformed into her true changeling form and brought Derpy back to the changeling colony. Now, the future Chrysalis told the new Chrysalis about how her plan had worked. Now the three were there and would wait for the perfect moment to reveal themselves.

It was almost time. Shining Armor and Cadence put their horns together, about to send off Chrysalis and her army back to the colony. This time, it would be different. Queen Chrysalis was about to re-write history! The three Chrysalises burst into the room, scaring Shining Armor and Cadence for a split second. There were now four chrysalises. The original Chrysalis, the Chrysalis from the TARDIS, the Chrysalis from the changeling colony, and finally the Chrysalis from the future. The original Chrysalis was still confused but the others told her not to worry and they would explain later. "Fools. You really think you could defeat the one and only Queen Chrysalis?" the future Chrysalis said "Think again." The colony Chrysalis whispered to the original Chrysalis to follow her lead.

All four now lightened up their horns. Twilight, Shining Armor, and Cadence all lit up their horns as well and it was quite a showdown. Even the power of love and friendship was no match for an entire changeling army AND four Queen Chrysalises! Now, everyone lay on the floor as the Chrysalises' power was so strong it knocked everyone unconscious.

The future Chrysalis had a surprised look on her face along with the others. She looked to the other Chrysalises. "W-we did it. We won."


	5. The Survivor

**Chapter 5: The Survivor**

"Take her away, minion!" said Queen Chrysalis to Colgate. Colgate nodded, transformed into an army changeling and flew Derpy away, deeper into the changeling colony. The Chrysalises went on with their plan. The Chrysalises would then go on to defeat Twilight, Shining Armor, and Cadence. Derpy, on the other hand, was still being carried by the changeling.

"W-where are you taking me?" Derpy asked. The changeling hissed. "To the dungeon." It said. Derpy got thrown inside a cell. It was very dark but she felt a pony creep up by her. Derpy began to feel scared but the pony somehow wasn't scaring her.

The pony began speaking. "Uh, hello there." The pony said. Derpy immediately recognized it. It was her own voice! Derpy knew this wasn't some sort of changeling. This was Derpy. She was talking to herself. "Are you from the past or future?" asked the first Derpy. The other Derpy replied "I don't think so…" The first Derpy started asking the other Derpy questions. "How did you get here?" "Well, I was with Dr. Whooves and Colgate. We came out of the TARDIS to stop Queen Chrysalis but then Colgate brought me here. She turned out to be a changeling.

Derpy was extremely clumsy but even she wasn't stupid. She knew what this was. This wasn't a Derpy from some other time. This was a Derpy from some other universe. This Derpy was from a parallel universe. This Derpy is from a parallel universe in which the Queen Chrysalises sent Derpy to the dungeon immediately while the main Derpy was from a universe in which she got sent to the dungeon much later. Both Derpy's now knew all this and without asking any questions started plotting ways to get out. One more thing that they both knew was that the dungeon must somehow not be affected by changes in the space-time continuum or else the first Derpy would have been erased from existence when time was altered. These Derpy Hooveses were sole survivors of the space-time alteration.

The changelings never expected to have a pony in their dungeons. They were made solely for changelings. They never counted on a Derpy Hooves to be there either. Derpy tried flying right out but crashed hard into the wall. Her head was spinning for a while but then the other Derpy joined in. They were both ramming into the wall. No changeling or even pony would try to break out by injuring themselves, that is, except Derpy. They kept flying hard into the wall until it began cracking. They continued at it until they broke the wall down.

The changelings were ready for them in case of some sort of break down so instead of fighting, the two Derpy Hooves made a run for it. They ran into where they left the TARDIS. The two got in. The TARDIS went to the exact same time they were in but in a different universe. The universe of the alternate Derpy. The main Derpy Hooves started fading. "I can't be in this universe. You'll have to go one without me. You have to warn everybody of Chrysalis. But promise me one thing." The fading Derpy said. The alternate Derpy Hooves was now crying that she was going to lose a good friend of hers, that friend being herself "What do I need to promise you?" "Promise me, you'll eat plenty of…" Derpy was almost completely faded away and then she disappeared with one last lingering word sticking in the alternate Derpy's presence "muffins…" Derpy continued to morn at the loss of her other self but she knew she had a mission to do. She would have to defeat Queen Chrysalis on her own.


	6. The Timelines

**Chapter 6: The Timelines**

Derpy was about to step out of the TARDIS when it suddenly started moving again. It was going back to present time. The doors opened and Derpy stepped out. She was inside of Dr. Whooves house. Everything looked normal. She heard muffed noises coming from a closet. It had a window in it and Derpy peaked in. It was Dr. Whooves and Colgate. Derpy wasn't sure whether to trust them or not though. Still, though, even if they were changelings, what could two extra Chrysalises do that four Chrysalises couldn't?

Derpy opened the door and took off some tape that was covering their mouths. "Oh thank heavens you're here. I really need your help!" Dr. Whooves said. Derpy was up against the wall, frightened. She didn't speak. "You did get that letter, right? I knew Queen Chrysalis was plotting something so I placed the letter in my mailbox, hoping you would find it." he continued. Derpy was still unsure but decided to talk "How do I know it's really you?" she asked. "Look outside. Have a see for yourself." Colgate replied for Dr. Whooves.

Derpy leaned outside the window. The skies were red and the clouds gray. All the ponies had chains on them and were being forced to work as slaves for the changeling army. They had completely overtaken Ponyville and possibly all of Equestria, although it was impossible to tell now. "You see all of the destruction right? Even as you were speaking to the fake me and the fake Colgate earlier, I was trapped in this closet. I, however, was not affected by the time alteration because my house has a time bubble as one might say. Time flows forever in here and nothing can change that, unless the bubble, of course, were destroyed. Chrysalis, however, did not know this and just left me tied up in here instead."

Derpy was no longer frightened. The way everything looked outside and Dr. Whooves' explanation was enough. Now she wasn't speaking but not from fright, but from shock. All of this was happening so quickly. "Oh, and the TARDIS has it's own time bubble as well. That's why _you_ weren't affected." Dr. Whooves continued. Finally, Derpy was able to snap out of her shocked state and fully untied both Dr. Whooves and Colgate.

"I know _exactly_ how to fix this. We can use my time bubble as a time explosion. However, if we are to do so, we must go to a point before _any_ time jumps or time landings were made. While Chrysalis was talking to you, I heard that she was planning on going back in time to the wedding. This means we must use the TARDIS to go to a point in time _before_ the part of the wedding you arrived at. Only you know where you arrived so only you know where you must go." Dr. Whooves said.

"Once there, you have to detonate the TARDIS yourself. I, unfortunately can not go with you. This is _my_ TARDIS and _my_ time bubble so if I change time with you, the very fact that I am telling you this right now might be erased from existence and space-time will cease to exist. You, on the other hand, have _nothing_ to do with any of these time jumps so you are the perfect candidate. You will have to go back alone, with the TARDIS and detonate it. Afterward, the TARDIS will go automatically go back to the present. Because you are from the timeline without Chrysalis' reign, nothing will happen to you as you are only restoring your own timeline. However, I can not guarantee that you will be in the present in time." Dr. Whooves continued.

"In other words, if you blow the time bubble up, and you're not in the present yet, you will be changed into the Chrysalis timeline for a split second. Once you're changed back with the result of the time bubble, you wont remember any of this. Hopefully, that wont happen and you'll be able to remember all the events of which occurred today. Or, not today, but you know what I mean. The last thing I must say is that whether you be in the present time for you to remember or not, I will not remember no matter what." Dr. Whooves continued to explain.

"The TARDIS' time bubble and the time bubble of my house are connected so when you detonate the TARDIS' time bubble, so will this one. When my time bubble explodes, I will no longer be protected from time anomalies. I may not be able to remember the brief friendship between you and me but I will be able to remember the events that have occurred here. Everything I just said 'I know how to fix this' to what I am saying right now is being recorded behind me. I need you to take it with you so that it does not get affected by time. If it does, that means you didn't get to the present in time and even you won't remember anything. However, if you are still protected in time, this recording should stay in tact. When you return to the present, I want you to come straight back here. I'll have no memory of you but all you'll have to do is give me this recording and I'll believe every word you say. We haven't got much more time." Dr. Whooves grabbed the recording and placed it in Derpy's hooves. Suddenly, the doors to Dr. Whooves' house burst open.

"Go. Now." Dr. Whooves said as he shoved Derpy into the TARDIS. Dr. Whooves was going to close the door on her when the changelings grabbed him. The changelings' horns glowed and then so did Dr. Whooves and Colgate. They screamed at the bottom of their lungs. The changelings began talking "We have direct orders from the queens to eliminate you. You are a threat to the mission and can not be tolerated." Dr. Whooves and Colgate were in dear pain but Dr. Whooves somehow managed to speak "Ahh! Go! Close the TARDIS and go off! Remember! Ahh! If you succeed, none of this will happen! We'll be fine! AHH!" He couldn't talk anymore. It was a terrible sight seeing her friends in pain but Derpy knew what she had to do. She closed the TARDIS and continued to hear screaming. Then, all of a sudden. There was a splat on the TARDIS. There was a semi-transparent window on it but it was no longer transparent. It was red. And, there was complete silence now. Derpy knew exactly what had happened and began crying. The changelings were now banging on the TARDIS trying to get it opened. This scared Derpy into realization and she set it to go back in time once more. This might have been her final time jump.


	7. The Fixer

**Chapter 7: The Fixer**

The TARDIS suddenly stopped. Derpy had reached her destination. She had now arrived at the moment where Twilight was claiming Princess Cadence to be evil and nopony believed her (even though Twilight was right!). Derpy remembered what was coming. It wasn't long before Twilight would be underground and Queen Chrysalis would start singing. If that were to happen, it would be too late as the past Derpy, fake Dr. Whooves, and fake Colgate would have arrived by then. No, she had to do it now. That's when Derpy realized something very important. Dr. Whooves never told her _how_ to detonate the TARDIS' time bubble!

There had to be _something_ Dr. Whooves had told her. Even just to _hint_ as to how to detonate the time bubble. That's when it hit her. Dr. Whooves had said something about "not being protected by time anomalies. For the time being, the TARDIS was protected from time anomalies. If Derpy could get a time anomaly to occur _inside_ of the TARDIS, she might just be able to cause a space-time explosion big enough to detonate the bubble! It was an incredibly dangerous plan that only somepony like Derpy could come up with. Even so, it wasn't like she had any other choice.

Derpy raced for the castle doors and found a ribbon. She grabbed it and ran inside. She saw Princess Cadence crying although she knew it to be Queen Chrysalis. She looked around and saw herself. It wasn't any of her selves that she had seen before. This pony was specifically the Derpy from the date of the wedding. It was perfect. She crept up to herself, blindfolded her, covered her mouth, and made her walk. If Derpy were to spoil something now, the time anomaly would occur _out_ of the TARDIS and a paradox would occur disrupting space-time where nothing could exist. She'd have to keep everything a secret until inside the TARDIS.

"Huh? Where did all the lights go?" said the blindfolded Derpy. Derpy began to whisper so that she wouldn't recognize her own voice "I can't tell you that just yet. But I promise you. You don't have to be scared. Also, I'll make sure you eat plenty of muffins if you help me out. No more talking, just walking." The Derpys walked around the corner of the castle and saw the fake Cadence making Twilight fall through the ground. She only had a few minutes before the singing was about to start. They had to hurry and began running. The TARDIS was now in view and the Derpys heard an explosion. They didn't know it but this was the explosion that Twilight had caused with her power which resulted in finding the real Princess Cadence.

Finally, they arrived at the TARDIS. The singing had now just started but the other TARDIS hadn't arrived yet. Obviously, the TARDIS arrived at some point while she was singing but not yet. They had no time to spare. Derpy had to make the blindfolded Derpy do something that would cause none of it to happen. Inside the TARDIS, Derpy took the other Derpy's blindfold off. "Derpy, I can't explain anything to you right now. You just need to make sure that if you ever get into this situation, you will never tell yourself to do what I'm telling you to do right now. Got it?" the main Derpy said. That was it. That would have created a paradox in itself but they were already in the time bubble. The paradox disrupted itself into it's own paradox still being contained by the TARDIS' time bubble. It was all over. A bubble couldn't contain a universe wide time paradox and began to explode. The Derpy who was blindfolded disappeared into thin air and the TARDIS began shaking.

At the exact same moment, Derpy heard a popping noise which she assumed to be the time bubble exploding, and she saw a great flash of light. Hopefully, it wasn't too late and the time bubble worked. Maybe, she had even kept her memory. She was unable to tell now. Her mind was racing and she was seeing absolutely everything that was going on. Time was moving rapidly. Chrysalises being erased from time. Dr. Whooves being erased. All errors in time were being fixed. All the events being pressed into Derpy's brain in a split second was too much and she fell into an unconscious state.

If Derpy were to wake up without any memories, the recording would have been erased from existence and nopony would be able to stop Queen Chrysalis. Everything would happen all over again. She had to. It was very hard but Derpy was somehow clinging onto her memories. Time was trying to wipe them away but Derpy tugged. She wouldn't let her precious memories leave. She had to remember. She couldn't let any of this happen again. Finally, time let go and Derpy was alright. And with all of her memories.

Derpy wasn't sure how long she was out but she did wake up eventually. She somehow wasn't in the TARDIS anymore. She woke up flying. She had a piece of paper in her hooves that said "Derpy Hooves, come to Dr. Whooves' house A.S.A.P.". This is how the whole event had started. She would have to somehow get Queen Chrysalis and her changeling away from the TARDIS so she could get the real Dr. Whooves and Colgate to listen to the recording. Derpy now had a plan.

Derpy flew over to Dr. Whooves' house but this time, instead of knocking on the door, she went through a window. Chrysalis and the changeling was not expecting this and she was able to burst the door which contained the real Dr. Whooves and Colgate, open. By this time, Chrysalis had now noticed them. "How did you know they were in there!" Chrysalis, in the form of Dr. Whooves asked. "Simple. All this time jumping has made me hungry and it's all your fault! THIS IS FOR THE MUFFINS!" Derpy yelled as she dove in towards Chrysalis in Dr. Whooves' form and rendered her a bit dizzy. Dr. Whooves and Colgate took care of the changeling in Colgate's form. Derpy told them to go into the TARDIS. They used it to go to the entrance of the Princess' castle. It would take a while for Chrysalis to get there without a TARDIS, perfect to listen to a recording. Without any questions, Derpy began playing the recording.

"I know _exactly_ how to fix this. We can use my time bubble as a time explosion." it began to say. Dr. Whooves was very intrigued as to why the recording was playing back something that he never recalled ever saying. It continued on for several minutes. "I'll have no memory of you but all you'll have to do is give me this recording and I'll believe every word you say. We haven't got much more time." it said and then the recording ended. Now Dr. Whooves began talking "So what you're telling me, or more so, what I'm telling myself, is that we need to stop those imposters, no?". Derpy confirmed his suspicions and made the TARDIS go to the Celestia's room. Now it was Colgate's turn.

"Your highness, we have no time to explain. This pony has confirmed our suspicions about the changelings." she said pointing to Derpy Hooves. "We can talk more about it later but for now we have to eliminate them. If they get a hold of our TARDIS, all we be lost. Everything had already been lost but this pony gave us all another chance. With time travel, we now have a chance to defeat the changelings once and for all! We'll need your help and the help of the elements of harmony."

Princess Celestia looked down at the three. "I can most certainly help. My sister can help too. The ponies you need, however, are those who have the spirit of the elements of harmony. Applejack, the spirit of Honesty. Rainbow Dash, the spirit of Loyalty. Rarity, the spirit of Generosity. Fluttershy, the spirit of Kindness. Pinkie Pie, the spirit of Laughter. And finally, Twilight Sparkle, the spirit of Magic. With their power and ours we might finally be able to vanquish their threat for good. The only problem is, is that if we banish them from Equestria again, what good will it do? They can easily come right back."

Derpy wasn't too sure about this but it was worth a say "Um, what if we use the time bubble? Now that the time bubbles exploded, everything turned back to normal which means the time bubbles are still here, right?" Dr. Whooves looked at Derpy with awe "For a pony who's very derpy, you seem to be very smart.". Derpy smiled. So did Princess Celestia and she began talking again "Very well. Gather the six ponies who contain the spirits of the elements of harmonies and go to Twilight's library home. I'll meet you there." She nodded and the three ponies got into the TARDIS and headed for Twilight's house. They had no idea where the others were so it was best just to find the pony who they did know where was. Once they found her, it would be easier to find the other five.

They headed straight for Twilight's door and knocked on it. "I've got it Twilight!" said Spike. "Thank you, Spike." Twilight said. Spike opened the door. "Hello there!" he said "Are you friends of Twilight's? She'll be down in just a second." "Well, we're more of friends of the Princess." Dr. Whooves said. In an instant, after Twilight heard the word Princess, she was at the door. Now Twilight spoke. "Please, come in."


	8. The Finders

**Chapter 8: The Finders**

The ponies walked into Twilight's house. "So, I hear you were sent by the Princess?" Twilight asked. "Yes, and we haven't much time to explain. We are in need of the spirits of the elements of harmony. Celestia told us that you are the spirit of the element of Magic. That means one down, five to go, correct?" Dr. Whooves partially explained. "And why do you need the elements of harmony?" asked Twilight again. "The changelings are back." Colgate told her. That was enough for Twilight. Chrysalis, queen of the changelings almost ruined her big brother's wedding with the best foalsitter in Equestria! She wouldn't let her do anything bad again. "Count me in! I know where all my friends live." Twilight said, running out. The other ponies followed.

The door slammed shut. "What about me?" asked Spike into the open and there was no response. "Hmph, I never get invited to do anything." he continued. He crossed his arms and sat down. There was a knock on the door. "Who is it?" said Spike in a moaning tone. "It's me, Spiky-wiky!" Rarity's voice said. Her voice was so soothing to Spike and he floated to the door and let her in. "Oh, um, hi Rarity." Spike began to blush. Rarity walked up to Spike. "Spike, I've been thinking. I know you have a crush on me so maybe we could go on a date?" she asked. Spike's eyes suddenly turned into giant red hearts. "I'd love to!" he yelled. "Wonderful! Hop onto my back." Rarity told him. He did just that and they walked out of Twilight's house.

The four other ponies were now at Rarity's house. They knocked on the door and Rarity opened it. They explained what was going on as quick as they could and Rarity was ready to wear her necklace again. They headed off into another direction.

Spike was still on Rarity. He didn't know it yet but this Rarity was an imposter. Rarity headed over to the real Rarity's house and went inside. Spike was still in a daze and didn't know what was going on. Rarity opened up a closet. "Now, Spike, how do you like THIS?" she yelled as she bucked Spike into the closet and closed it. "Huh? Who are you! That hurt!" Now Rarity's voice was different. It sounded more like Chrysalis'. "Fool. Now that you're trapped in there, Twilight will believe anything I say as you." Chrysalis began transforming herself into Spike as she spoke. "Do you really think Rarity would have gone out with you? You're so gullible." she said as Spike. Chrysalis slammed Rarity's door and returned to Twilight's house where she would wait for them all to return.

The ponies now had everypony, except for Rainbow Dash. It was impossible to find her without flying so they had to get into a hot air balloon. Once in the air, Fluttershy helped fly it and Pinkie Pie kept a keen eye out for her. Suddenly, Pinkie's tail began a-twitch-a-twitchin'. "Oh boy, that's not good..." Twilight said, looking at Pinkie's tail. Suddenly, the balloon plummeted straight for the ground. It hadn't burst, it was just floating downward at a rapid speed. Something had obviously fallen on it. When they all walked out, they noticed a pony was on top of the balloon. It was none other than Rainbow Dash. "Well ah'll be. Pinkie's tail even works when it's a pony fallin' out of the sky. Well at least we found Rainbow." Applejack said. Rainbow Dash slowly got up and rubbed her head.

"Ugh. What are you doing with a hot air balloon in the middle of the sky!" Rainbow yelled. Twilight went up to her and explained what had happened. Like the other ponies, Rainbow was fully ready to kick some changeling butt. They had now gathered all the ponies. They now headed back to Twilight's house. The door was already opened. They went inside and Chrysalis (in the form of Spike) was there, expecting them. "Oh, hey Twilight." Chrysalis said. "Hey Spike, have you seen Queen Chrysalis recently? I reckon she's gotta be around here somewhere..." Applejack asked.

That's when Princess Celestia came inside. Princess Luna was behind her. Following her were the two newly married. Prince Shining Armor and Princess Cadence. "I decided to bring these two along. They could probably help in defeating Chrysalis." Celestia said. Twilight went and hugged both Shining Armor and Cadence. They had been on their honeymoon and hadn't seen them sense the wedding! Chrysalis knew that with these two around, she could easily be defeated again. "If you're looking for Queen Chrysalis, I think I might know where she is!" Chrysalis said as Spike. She led them up to the attic and let the ponies all go in first. Then she locked the door on them and transformed back into Chrysalis. "You're just as foolish as the dragon. Goodbye now." Chrysalis said, heading outside to look for the TARDIS. "You wont get away with it! I bet all my muffins on it!" Derpy shouted. Dr. Whooves looked to Derpy. "Are muffins all you talk about?" he asked."But...I like muffins..." she sighed.

The TARDIS was right outside of Twilight's house so it didn't take long for Chrysalis to spot it. Then again, it didn't take long for the unicorns to teleport everypony outside. The ponies surrounded the TARDIS and Queen Chrysalis stood in front of them. It wasn't looking good for her now. Shining Armor and Cadence put their horns together like before and the mane six began using the elements of harmony. Together, they banished Queen Chrysalis back to the changeling colony. "Whew. That sure was close." Twilight said. Queen Chrysalis then reappeared right in front of them with the power of her horn. "You know you'll never get rid of pony get inside the TARDIS, I'll explain later." Dr. Whooves said.

The ponies hurried inside the TARDIS before Chrysalis could do anything to stop them. Once inside he told Shining Armor and Cadence to use their horns again. They did and sent Chrysalis flying. Afterward, the mane six used their powers and even Princess Celestia and Princess Luna joined in with the magic of their horns. From inside the TARDIS, it caused a chain reaction big enough to make the TARDIS' time bubble explode. Just as Dr. Whooves wanted it to, the time bubble followed Chrysalis to the colony and formed a solid bubble around it. Almost like a fish bowl but in this case, a changeling bowl. And they couldn't get out of it.

"Is that it?" Derpy asked. Princess Celestia opened the door. "Yes, I believe it is." she replied. Derpy looked happy and said "Yay! I get to keep my muffins!" Dr. Whooves facepalmed and Colgate couldn't help but laugh. "I'll head out to make sure." Celestia continued. She spread out her wings and flew away. "I'll come with you sister." Luna said as she followed. Pinkie Pie was laughing uncontrollably as soon as the changeling went away making sound effects that sounded like the time bubble exploding while Fluttershy hid in the corner. "Hooey! That was some mighty fine teamwork don't ya think, sugar cube?" said Applejack. "If it were up to me, I'd just give her a punch on the left, a punch on the right, and then an uppercut to put her in her place!" Rainbow Dash said, still with lots of enthusiasm. "That was pretty interesting actually. I assume everything is fixed?" Twilight said looking directly at Dr. Whooves, Colgate, and Derpy.

"Well, to what we know right now, yes, everything is fine. Chrysalis appears to be trapped, my TARDIS seems to be fine even without a time bubble, and none of us have disappeared from existence. I think everything is perfect." Dr. Whooves said. "In that case, I guess it's time to bid you ado. Thanks for all the information. We couldn't have defeated Chrysalis for good without you." Twilight replied. Dr. Whooves, Colgate, and Derpy nodded. The mane six exited the TARDIS and headed back home. Dr. Whooves took the TARDIS back to his home so that he could begin rebuilding the time bubble for his TARDIS. Most everything Derpy had heard from the fake Dr. Whooves was a lie but there was one thing that wasn't and Derpy was soon to find out.


	9. The Conspiracy

**Chapter 9: The Conspiracy**

"Please, Derpy Hooves, stay here." Dr. Whooves said, motioning Derpy to stay inside the TARDIS. The TARDIS went back to his house and the three of them went inside. "Now Derpy, I'm aware that you had to time jump. Please, tell me everything." Dr. Whooves said. After seeing Chrysalis being defeated for good, Derpy was sure that she could trust _this_ Dr. Whooves. What were the odds of it being another trick? Derpy did just what he told her to do and told him everything. From the fake Dr. Whooves all the way to exploding time bubbles. Dr. Whooves was listening attentively the whole time. "So you went back and forth through times that much? And even had contact with yourself from a different timeline?" Dr. Whooves asked even though he already knew the answer. Derpy nodded. "That surely can't be good for a pony. Are you sure you're alright?" Dr. Whooves asked. Derpy nodded again. "Well, there is one very important thing about what you're telling me. When you first met Chrysalis, when she was in my form, most of what she told you was true." Dr. Whooves began.

"Princess Celestia was on a secret mission. She was trying to find out if the changeling threat was really gone but she didn't want to tell anypony. I thought she wasn't telling anypony because there was something beyond changelings. Possibly even beyond Equestria. I thought there was a conspiracy going on. I found out that I was wrong, however, that wasn't until after I did some snooping around with my pal Colgate. We used the TARDIS to figure out what Princess Celestia was planning and I didn't find anything conspiracy worthy. I eventually stopped snooping and decided to talk to her face to face." Dr. Whooves explained.

"Princess Celestia somehow knew I was snooping. She knew it even while I was bending the laws of time and space with the TARDIS. I don't know how nor do I think I'll ever know how but she knew. She _also_ knew that she had no choice but to confess everything to me. She knew I would eventually find out regardless. When I went to speak to her she told me her plans about finding the changelings. At first I thought she was just hiding her true plans again but she then asked me to help. Both Colgate and I. Apparently she figured that with the TARDIS, we would have a much better chance at finding the changelings so she chose us." Now Dr. Whooves' face began to look grim.

"However, if he chose to accept her mission, we would have to keep it a complete secret. This is why Princess Celestia wasn't sure about accepting you when the fake Colgate and I were asking you to join our team. I wouldn't have expected it but she somehow accepted. She must have a lot of trust in us. Anyway, my point is that now you know all about it. Normally, in cases like these, we would go back in time and stop you from ever finding out about any of this. Problem with that is that you played the key role in all of this. Without you, Chrysalis could have found some other pony to help her out and you would have never been able to stop her. You're the reason everything was fixed. You're the reason that we're all alive here speaking right now. We can't erase your memory and change time. You're forcefully part of our team now. Unfortunately, this means you can't tell anypony about anything anymore. The only ponies you can talk to about time travel, space travel, and the TARDIS right now is Princess Celestia, Colgate, and I. You can't even tell Princess Luna. She has no idea about Celestia's plans. You can talk about anything else. Even the changelings and Queen Chrysalis. Just nothing specifically about her mission. Got it?" Dr. Whooves asked.

Dr. Whooves had a habit of talking a lot and everything going above Derpy's head although she understood most of it and nodded. "Very well. Welcome aboard then." Colgate said. "The last thing we need to do is update with the Princess." said Dr. Whooves and they all got into the TARDIS once more and headed for Princess Celestia's castle.

Once inside, they went straight to Princess Celestia's chamber. She stepped down to be right next to them. "I am aware that Derpy now knows our secret." she said and Dr. Whooves nodded. "Well, I have to apologize. I hate doing things like this to my own subjects. Just trust me when I saw I love you all dearly. However, I have no use for you anymore. You can have no recollection of this." Celestia continued to say. "We have already told you, we can't go back in time and stop us from knowing about it. That will change everything and the changelings will be in power." Dr. Whooves said. "Who said anything about time travel?" Celestia argued. She pulled out a pen. "Do you see this? It's a really cool looking pen, is it not?" she asked. Derpy was in awe. If was really cool and futuristic looking. All three of them were staring at it. Princess Celestia closed her eyes and pressed the end of it. A bright red flash of light came out of it and blinded the three ponies for a few minutes. They were practically unconscious.

Princess Celestia grabbed them and put them in the TARDIS. She set it to go back to Dr. Whooves house. It soon disappeared and Celestia was alone once more. She sighed. "I hate doing that to my friends. I just can never let them learn about my true motives. It would become a great disaster..." she said as she walked back up to her throne. There was, however, one thing that the Princess wasn't counting on. After Derpy had finished playing the recording for Dr. Whooves much earlier, instead of pressing the off button, she hit the record button. The recorder had been recording everything from talking to Dr. Whooves to talking to Princess Celestia. They had forgotten all their memories about time travel but they would soon recover some of them after finding the recorder. Given the fact that it was Derpy who had it, it could have been a very long time before they did. Either way, everything was now calm in Equestria with no threats from anypony. Even Celestia didn't want to harm anypony, she just had a very big secret. Unfortunately, nopony would ever know...

Meanwhile in Rarity's boutique...

"Hello! Is there anypony there!" Spike said pounding on the closet door. "Rarity? Are you here?" Spike continued with no response. The mane six were all celebrating Chrysalis' defeat at Sugar Cube Corner. "Awww..." Spike moaned, sitting down, realizing there still wasn't anypony around.


	10. Credits

**Actual Show Credits:**

**My Little Pony: Friendship is Magic:**

**Created by:**

Lauren Faust

**Written by:**

Lauren Faust

Amy Keating Rogers

Cindy Morrow

Chris Savino

Meghan McCarthy

Charlotte Fullerton

M. A. Fullerton

Dave Polsky

Merriwether Williams

**Directed by:**

Jayson Thiessen

James Wootton

**Executive Producers:**

Lauren Faust

Chris Bartleman

Blair Peters

Kirsten Newlands

Beth Stevenson

Stephen Davis

**Composers:**

William Kevin Anderson

Daniel Ingram

Steffan Andrews

**Voice Actors:**

Tara Strong

Ashleigh Ball

Andrea Libman

Tabitha St. Germain

Cathy Weseluck

Nicole Oliver

Michelle Creber

Meadeleine Peters

Claire Corlett

John de Lancie

**Production Companies:**

DHX Media/Vancouver

Hasbro Studios

Top Draw Animation

**Distributor:**

The Hub

**FanFiction Credits:**

**Written by:**

Joshua Simon

**Shows Used:**

My Little Pony: Friendship is Magic

**Disclaimer:**

I do not own the rights to anything that is or is related to My Little Pony.

**Final Comment:**

**Thank you to everyone who read and enjoyed my fanfiction! It was so much fun to write this fanfiction so I hope you enjoyed it! Thank you again!**


End file.
